My PhD research is concerned with the development of statistical methodology for the integration of multiple ‘omics datasets (e.g. genomic, transcriptomic, proteomic, etc.) in personalised medicine.
My goal is to tackle some of the challenges presented by the identification of relevant patient subgroups (e.g. patients that might be expected to respond similarly to treatments) on the basis of those datasets.
First, when combining different types of ‘omics datasets, it is crucial to take into account the different nature of each dataset. For this reason, I am developing integrative clustering methods that explicitly weigh the contribution of each dataset to the final clustering according to the amount of information that it contains, and that allow to combine datasets of different type (e.g. continuous, categorical, etc.). These methods are based on the idea that the output of classical statistical techniques such as model-based Bayesian clustering can be used in combination with kernel methods from the machine learning literature to find a meaningful global clustering that summarises all the information available.
Second, because genomics datasets comprise measurements taken on a very large number of variables, many different patient subgroups can usually be identified, depending on which variables we include in our analysis. For this reason, I am also working on integrating genetic information with data on specific patient outcomes, to ensure that we identify truly relevant patient subgroups. To do so, I have generalised the method above to the supervised case, and I am now going to implement a variational inference algorithm for outcome-guided model-based Bayesian clustering, as an alternative to that.
On a more applied note, I am participating in a study on cardiovascular disease. My role in the project is to analyse data collected at the Cambridge Blood Donor Centre with the statistical methods mentioned above, to define a personalised cardiovascular disease risk score.
Cabassi, A., Richardson, S., Kirk, P. D. W. Kernel learning approaches for summarising and combining posterior similarity matrices. In preparation.
Cabassi, A., Seyres, D., Frontini, M., Kirk, P. D. W. Penalised logistic regression for multi-omic data with an application to cardiometabolic syndrome. In preparation.
High performance, large scale regression
During my internship at The Alan Turing Institute, I explored different methods and libraries to perform high-performance, large-scale regression on a supercomputer, with particular focus on Apache Spark and TensorFlow. The internship was funded by Cray Inc and carried out in close collaboration with the Cray EMEA Research Lab. You can find more details about our findings on the blog and the official webpage of the project.
Permutation tests for functional and network data
Cabassi A., Casa A., Fontana M., Russo M., Farcomeni A., 2018. Three Testing Perspectives on Connectome Data. In: Canale A., Durante D., Paci L., Scarpa B. (eds) Studies in Neural Data Science. Start Up Research 2017. Springer Proceedings in Mathematics & Statistics, vol 257. doi:10.1007/978-3-030-00039-4_3.
I am a mentor at Lead The Future, a nonprofit providing 1:1 mentoring to high-potential Italian students, since 2019. This year, I am mentoring 2 undergraduate and 3 graduate students at top European universities and institutions. Forbes talked about Lead The Future in this article (in Italian).
A.I.M. (Associazione Ingegneri Matematici) is a student society with the goal of promoting the concept of Engineering Mathematics and creating a network between students and alumni from Politecnico di Milano, to facilitate the exchange of ideas, opinions and advice about the academic and professional life. Find out more about what we do with this amazing presentation!
I was the president of the committee in 2014 and continued contributing to the Association ever since. I currently organise events for A.I.M. members in London. If you are interested in joining us, let us know by sending an email to firstname.lastname@example.org.